Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

(2019) Brian K. Trevelline et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Linking a mutation to survival in wild mice

(2019) Rowan D. H. Barrett et al.   SCIENCE

A Single Interacting Species Leads to Widespread Parallel Evolution of the Stickleback Genome

(2019) Sara E. Miller et al.   CURRENT BIOLOGY

Detecting the Macroevolutionary Signal of Species Interactions

(2019) Luke J. Harmon et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Diet influences host–microbiota associations inDrosophila

(2018) Benjamin Obadia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural selection and the predictability of evolution inTimemastick insects

(2018) Patrik Nosil et al.   SCIENCE

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs

(2018) Maelle Sevellec et al.   Microbiome

Role of the Gut Microbiome in Vertebrate Evolution

(2018) Thomas J. Sharpton   mSystems

Bacterial Methionine Metabolism Genes Influence Drosophila melanogaster Starvation Resistance

(2018) Alec M. Judd et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatiotemporal dynamics and genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

(2018) Subhash Rajpurohit et al.   MOLECULAR ECOLOGY

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota

(2018) Christopher A. Gaulke et al.   mBio

From low to high gear: there has been a paradigm shift in our understanding of evolution

(2018) David N. Reznick et al.   ECOLOGY LETTERS

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong responses of Drosophila melanogaster microbiota to developmental temperature

(2017) Neda N. Moghadam et al.   FLY

Gut microbial communities of American pikas (Ochotona princeps ): Evidence for phylosymbiosis and adaptations to novel diets

(2017) Kevin D. Kohl et al.   JOURNAL OF ANIMAL ECOLOGY

Life history and eco-evolutionary dynamics in light of the gut microbiota

(2017) Emilie Macke et al.   OIKOS

Evolution of flower color pattern through selection on regulatory small RNAs

(2017) Desmond Bradley et al.   SCIENCE

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia

(2017) Rama K. Simhadri et al.   mSphere

What genomic data can reveal about eco-evolutionary dynamics

(2017) Seth M. Rudman et al.   Nature Ecology & Evolution

Adaptive dynamics of cuticular hydrocarbons inDrosophila

(2016) S. Rajpurohit et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative population genomics of latitudinal variation inDrosophila simulansandDrosophila melanogaster

(2016) Heather E. Machado et al.   MOLECULAR ECOLOGY

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation inDrosophila melanogaster

(2016) Alan O. Bergland et al.   MOLECULAR ECOLOGY

How multi-partner endosymbioses function

(2016) Angela E. Douglas   NATURE REVIEWS MICROBIOLOGY

Gut Microbiotas and Host Evolution: Scaling Up Symbiosis

(2016) Michael Shapira   TRENDS IN ECOLOGY & EVOLUTION

Can Population Genetics Adapt to Rapid Evolution?

(2016) Philipp W. Messer et al.   TRENDS IN GENETICS

Microbes Drive Evolution of Animals and Plants: the Hologenome Concept

(2016) Eugene Rosenberg et al.   mBio

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions

(2016) Melinda L. Koyle et al.   Jove-Journal of Visualized Experiments

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

(2015) Karen E Sullam et al.   ISME Journal

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome

(2015) Jun Wang et al.   Nature Communications

Symbiont infection affects whitefly dynamics in the field

(2014) Peter Asiimwe et al.   BASIC AND APPLIED ECOLOGY

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

(2014) Daniel I. Bolnick et al.   ECOLOGY LETTERS

A highly pleiotropic amino acid polymorphism in theDrosophilainsulin receptor contributes to life-history adaptation

(2014) Annalise B. Paaby et al.   EVOLUTION

Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

(2014) M. Sevellec et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

(2014) J. M. Chaston et al.   mBio

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

(2013) Peter D. Newell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Experimental evidence for ecological selection on genome variation in the wild

(2013) Zachariah Gompert et al.   ECOLOGY LETTERS

Biotic interaction strength and the intensity of selection

(2013) Craig W. Benkman   ECOLOGY LETTERS

Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations ofDrosophila melanogaster

(2013) Martin Kapun et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish

(2012) Ivana Semova et al.   Cell Host & Microbe

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

(2012) Alison F. Feder et al.   PLoS One

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Lactobacillus plantarum Promotes Drosophila Systemic Growth by Modulating Hormonal Signals through TOR-Dependent Nutrient Sensing

(2011) Gilles Storelli et al.   Cell Metabolism

Bacterial symbionts as mediators of ecologically important traits of insect hosts

(2011) HEIKE FELDHAAR   ECOLOGICAL ENTOMOLOGY

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling

(2011) S. C. Shin et al.   SCIENCE

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

(2010) B. Kolaczkowski et al.   GENETICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Commensal bacteria play a role in mating preference of Drosophila melanogaster

(2010) G. Sharon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

REPRODUCTIVE DIAPAUSE AND LIFE-HISTORY CLINES IN NORTH AMERICAN POPULATIONS OF DROSOPHILA MELANOGASTER

(2008) Paul S. Schmidt et al.   EVOLUTION

Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell

(2008) Y. Hongoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster

(2008) P. S. Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE